The Sonics, who led by 21 points at the start of the third quarter, saw the Hawks fight back to tie the score at 88-88 on a 3-pointer by Steve Smith with 15.1 seconds left.
After Baker's winning shot, Tyrone Corbin inbounded from midcourt and Christian Laettner's 3-point attempt from the right corner bounced off the rim.
Baker and Detlef Schrempf, returning after a four-game absence because of a bruised throat, each had 17 points and Gary Payton a season-high 15 assists for the Sonics.
For the Hawks, Smith scored 21 points and Laettner 20, while Dikembe Mutombo had 14 rebounds.
Schrempf, who was injured when he was hit in the throat by an elbow in practice, also had 10 rebounds.
Hersey Hawkins added 12 points and Sonics reserves Aaron Williams and Dale Ellis had 11 and 10, respectively. Henderson added 17 for Atlanta.
The Hawks rallied to tie the score at 80-80 on a 3-pointer from Smith with 4:10 left to cap a 10-2 run.
After that, Baker had a layup with 3:06 left and Hawkins sank two free throws with 2:30 remaining to put Seattle in front 84-80 before Laettner had a three-point play with 1:42 to go and Henderson scored on an offensive rebound put-back with 1:22 left to give Atlanta an 85-84 lead.
Two free throws by Hawkins with 1:17 to go and two more by Schrempf with 29.7 seconds left put Seattle in front 88-85 before Smith's tying 3-pointer over Sam Perkins.
In the third quarter, the Hawks had runs of 9-0 and 8-0 and trailed 71-63 after Smith's 3-pointer with 27.4 seconds left before Sam Perkins of Seattle made a 3-pointer with 8.1 seconds to go. The Sonics led by 21 61-40 after Payton's 3-pointer to open the second half.
The Sonics took an 18-point lead in the second quarter when they hit 13 of 17 shots and scored the first 10 points of the period.
Ahead 26-23 after the first period, the Sonics opened the second quarter with a 3-pointer from Ellis, two dunks and a free throw by Williams, a 17-footer by Ellis and a five-footer by David Wingate.
Williams had a layup on a pass from Payton with 4.8 seconds left in the first half to give Seattle a 58-40 lead.
NOTES: Schrempf and Atlanta's Chuck Brown each received technicals when they had to be separated after locking arms under the Atlanta basket with 6:11 to go in the second quarter. Schrempf was upset because he felt Brown threw at elbow at him. ... The Hawks beat Seattle 89-87 in Atlanta in the teams' first game of the season Nov. 11. ... Payton had 13 of his assists in the first half when the Hawks had eight assists. ... Sonics center Jim McIlvaine had six points, four blocked shots and six rebounds in 18 minuteagainst Mutombo, who finished with eight points and four blocked shots in 30 minutes. Mutombo leads the NBA in blocked shots. McIlvaine did not play in the final quarter.
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